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Dr Matthew John Wakefield

Research Officer

+61 3 9345 2631

wakefield@wehi.edu.au

Research Activities:

Matthew Wakefield works on the application of comparative genome analysis to the evolutionary events that occured early in mammalian evolution and their use in identifying medically important genes and genome features. This work encompasses phylogentic footprinting, adaptive evolution, and exaptation of repeat elements into regulatory networks.

He was an author on the proposal to sequence the genome of a model Australian marsupial (Macropus eugenii - the tammar wallaby) and continues to work in collaboration with the ARC Centre for Kangaroo Genomics and the Kangaroo Genome Project.

Other projects include:

Adaptive evolution of BRCA1 in ancestral mammals in collaboration with Simon Easteal, Gavin Huttley and Alexander Isaev at the Australian National University.
Evolution of marsupial and monotreme cone visual pigments
X-chromosome inactivation
The evolution of mammalian sex chromosomes
Exaptation of transposable elements
Custom Microarray and sequencing platforms for transcript analysis

He is the primary author of the Vestige maximum likelihood phylogenetic footprinting package that is built using the PyCogent toolkit and a contributor to the PyCogent package.

Recent Publications

Cheng Y, Wakefield MJ, Siddle H, Coggill PC, Herbert C, Beck S, Belov K and Eldridge MDB. (2008)
Isolation and characterization of 10 MHC Class I-linked microsatellite loci in tammar wallaby (Macropus eugenii)
Molecular Ecology Resources In Press

Warren WC, Hillier LW, Graves JAM, Birney E, Ponting CP, Grutzner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang S, Heger A, Locke D, Miethke P, Waters PD, Veyrunes F, Fulton L, Graves T, Puente XS, Lopez-Otin C, Ordonez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Aslop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Renfree M, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell N, Buschiazzo E, Jentzsch IV, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison E, Sachidanandam R, Smith C, Stark A, Kheradpour P, Hannon G, Rens W, Ferguson-Smith M, Lefevre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhard R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux J, Niwa H, Sekita Y, Flicek P, Webber C, Hardison R, Washington University Genome Sequencing Center, Mardis ER & Wilson RK. (2008)
Genome analysis of the platypus reveals unique signatures of evolution
Nature 453(7192):175-183

New York Times ABC News BBC World The Age Nobel Intent New Scientist ABC Science Video: ABC News ABC News (Extended) Audio: ABC Radio 'AM'

Wakefield MJ, Anderson M, Chang E, Wei K-J, Kaul R, Graves JAM, Grutzner F and Deeb SS (2008)
Cone Visual Pigments of Monotremes: Filling the Phylogenetic Gap
Visual Neuroscience 25 In Press
doi:10.10170/S0952523808080255

Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG, Easton BC, Hamady M, Liu Z, Lozupone C, Sammut R, Smit S, Wakefield MJ, Widmann J, Wikman S, Wilson S, and Huttley GA (2007)
PyCogent: a toolkit for making sense from sequence
Genome Biology 8:R171
Online Resources: PyCogent SourceForge Repository

	Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, Pollock DD, and Jurka J (2007) Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica Genome Research 17:992-1004.
	Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SMJ, Sharpe T, Baker M, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC, Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, Graves JAM, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K (2007) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences Nature 447:167-177.
	ABC Online, ABC Science, BBC News, Nobel Intent, The Australian (10th May Page 8), The Sydney Morning Herald (10th May Page 12), COSMOS, New Scientist, ABC Regional - AM, The Science Show

Huttley GA, Wakefield MJ, and Easteal S (2007)
Rates of genome evolution and branching order from whole genome analysis.
Molecular Biology and Evolution 24:1722-1730
Open Access Article

Hore T, Koina E, Wakefield MJ, and Graves JAM (2007)
XIST is absent from the X chromosome, and its flanking region is disrupted in non-placental mammals
Chromosome Research 15:147-161

El-Mogharbel N, Wakefield M, Deakin JE, Tsend-Ayush E, Grutzner F, Alsop A, Ezaz T, Marshall Graves JA (2007)
DMRT gene cluster analysis in the platypus: New insights into genomic organization and regulatory regions.
Genomics 89:10-21

full publication list

ISI Researcher ID A-7795-2008